Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
René L. Warren,J. Douglas Freeman,Thomas Zeng,Gina Choe,Sarah A. Munro,Richard D. Moore,John R. Webb,Robert A. Holt +7 more
TLDR
It is shown that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy, and a new, directly measured, lower limit on individual T-cell repertoire size is established.Abstract:
Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naive (CD45RA+/CD45RO-) and memory (CD45RA-/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.read more
Citations
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Composition and Variation Analysis of the TCR -Chain CDR3 Repertoire inSystemic Lupus Erythematosus Using High-Throughput Sequencing by Sui,et al
TL;DR: 2Clinical Medical Research Center, the Second Clinical Medical College of Jinan University (Shenzhen People’s Hospital), Shenzhen, Guangdong, P.R China.
Dissertation
Quantifying the development, size, and repertoire diversity of T cell populations
TL;DR: The aims of this thesis are to quantify the sizes of Tcell populations, to develop tools to measure the diversity of T cell repertoires, and to describe how T cell populations develop in neonatal mice.
Posted ContentDOI
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition
Dina Schneidman-Duhovny,Natalia Khuri,Natalia Khuri,Guang Qiang Dong,Michael B. Winter,Eric Shifrut,Nir Friedman,Charles S. Craik,Charles S. Craik,Kathleen P. Pratt,Pedro Paz,Fred Aswad,Andrej Sali,Andrej Sali +13 more
TL;DR: An integrative approach to predict T-cell epitopes that computationally combines information from three stages of the humoral immune response pathway: antigen cleavage, MHCII presentation, and TCR recognition, resulting in an increased accuracy of epitope predictions.
Patent
Immune repertoire profiling
TL;DR: In this article, a method for determining nucleotide sequences of a first polynucleotide and a second polynotide was proposed, where the first template oligonucleotide is annealable to the second template oligoneuclidean.
Journal ArticleDOI
The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling
TL;DR: In this paper , the authors developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal ( https://github.com/smiranast/iROAR ).
References
More filters
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
Journal ArticleDOI
T-cell antigen receptor genes and T-cell recognition.
Mark M. Davis,Pamela J. Bjorkman +1 more
TL;DR: This view of T-cell recognition has implications for how the receptors might be selected in the thymus and how they (and immunoglobulins) may have arisen during evolution.
Journal ArticleDOI
Nomenclature for factors of the HLA system, 2010.
Steven G.E. Marsh,E. D. Albert,Walter F. Bodmer,Ronald E. Bontrop,Bo Dupont,Henry A. Erlich,Marcelo Fernandez-Vina,Daniel E. Geraghty,Rhonda Holdsworth,Carolyn Katovich Hurley,M. Lau,Keun-Seok Lee,Bernard Mach,Martin Maiers,Wolfgang R. Mayr,Carlheinz Müller,Peter Parham,Effie W. Petersdorf,Takehiko Sasazuki,Jack L. Strominger,A. Svejgaard,Paul I. Terasaki,Jean-Marie Tiercy,John Trowsdale +23 more
TL;DR: This report documents the additions and revisions to the nomenclature of HLA specificities following the principles established in previous reports.